Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_084687665.1 OLEAN_RS06545 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= reanno::SB2B:6938540 (460 letters) >NCBI__GCF_000967895.1:WP_084687665.1 Length = 449 Score = 194 bits (493), Expect = 5e-54 Identities = 134/440 (30%), Positives = 219/440 (49%), Gaps = 28/440 (6%) Query: 6 QDTISALQAMDAAHHLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWCVN 65 Q + S A D H HP++ A+ ++ +E A+GVY+ A G +L+D M+ W Sbjct: 20 QTSASDALAYDQQHLWHPYSSFAN-KEQAVWPVESAKGVYLTLADGTELIDGMSSWWSTV 78 Query: 66 VGYGRKSIADAAYAQLQTLPFYNNFFQCTHEPAIRLASKIASLAPGHMNRVFFTGSGSEA 125 GY + A Q + + F THEPAI LA K+ L P +N+VF + SGS A Sbjct: 79 HGYSHPRMVKAISEQAAKMS-HVMFGGLTHEPAINLAYKLVQLTPEGLNKVFLSDSGSVA 137 Query: 126 NDTNLRMVRRYWDLKGMPSKKTIISRKNAYHGSTVAGASLGG--MGFMHQQGDLPIPGIV 183 + ++M +Y +G K +I+ K YHG T+ SL G H DL Sbjct: 138 VEVAVKMAIQYQQARGKSEKTKLIALKKGYHGDTLGAMSLCDPTTGMHHLFSDL------ 191 Query: 184 HIDQPYWFGEGRDMSPEAFGIKTAQALEAKILELGEDKVAAFIAEPF-QGAGGVIIPPDS 242 + Q ++ E + +A+ + + L + LE K+AA I EP QGAGG+ + Sbjct: 192 -LAQQFFIREPQITFDQAWHDEDIEPLR-QCLEKNHQKIAALILEPIVQGAGGMRFYHPT 249 Query: 243 YWNEIKRILEKYNILFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGV 302 Y +++ ++Y++L I DE+ +GFGR+G FA + G+ PD++ + K +T+GY+ + Sbjct: 250 YLKRARQLCDEYDVLLIADEIATGFGRSGKLFACEHSGISPDILCVGKALTAGYMTLAAT 309 Query: 303 IVSDRVADVL-ISDGGEFAHGFTYSGHPVAAAVALENIRILEEERLVDKV-RTDTGPYLQ 360 + +D +AD + + G F HG T+ +P+A A A E++ +L + +V R + G L+ Sbjct: 310 LTTDHIADTISAGEAGCFMHGPTFMANPLACAAANESLSLLIDNNWQAQVERLERG--LE 367 Query: 361 DRLQTLSAHPLVGEVRGMGMVGAIELVADKHSMVRFGSEISAGMLCREACIESGLVMRAV 420 L V +VR +G +G IE+ M R + ACI G+ +R Sbjct: 368 AGLSLAKTLDAVADVRVLGAIGVIEM-KKAVDMKRI----------QPACIAQGIWLRPF 416 Query: 421 GDTMIISPPLCITRDEIDEL 440 G + I P +T E+++L Sbjct: 417 GKLVYIMPAYVMTDGELEKL 436 Lambda K H 0.321 0.137 0.408 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 464 Number of extensions: 21 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 460 Length of database: 449 Length adjustment: 33 Effective length of query: 427 Effective length of database: 416 Effective search space: 177632 Effective search space used: 177632 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory